Structurally heterogeneous materials, both inorganic and organic, are widely used. The development of new materials represents a significant interest in engineering. Simulation-based, computer-aided modeling has proved to be time and cost-saving and has already been used in modeling and studying the properties of different classes of materials. This paper proposes the online laboratory’s architecture for modeling and studying the properties of structurally heterogeneous materials. The SDLC methodology designs system modules, Use-Cases and UI/UX framework. As the outcome, the deployment diagram is proposed with a separate Web user interface, backend simulation engine, and persistent data storage. Such web applications could help researchers and students perform simulation experiments using state-of-the-art Monte Carlo methods with the support of classical and quantum computer hardware. As we begin to reach the limits of classical computing methods, quantum computing algorithms could broaden the reach of simulation modeling. The schematics of random number generation according to the normal distribution law using an IBM quantum computer is described as one of the possible improvements to classical Monte Carlo.